Merge pull request #622 from BioJulia/patch-1

BioStructures.jl compat
BioJulia · Jul 13, 2024 · 086059d · 086059d
2 parents fc291e5 + 70060e1
commit 086059d
Show file tree

Hide file tree

Showing 5 changed files with 9 additions and 9 deletions.
diff --git a/Project.toml b/Project.toml
@@ -37,7 +37,7 @@ TensorCast = "02d47bb6-7ce6-556a-be16-bb1710789e2b"
 
 [compat]
 BioAlignments = "2, 3"
-BioStructures = "2, 3"
+BioStructures = "4"
 ColorSchemes = "3"
 ColorTypes = "0.11"
 Colors = "0.12"

diff --git a/README.md b/README.md
@@ -35,7 +35,7 @@ using GLMakie
 using BioStructures
 struc = retrievepdb("2vb1") |> Observable
 ## or
-struc = read("2vb1.pdb", BioStructures.PDB) |> Observable
+struc = read("2vb1.pdb", BioStructures.PDBFormat) |> Observable
 
 fig = Figure()
 plotstruc!(fig, struc; plottype = :ballandstick, gridposition = (1,1), atomcolors = aquacolors)

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -64,7 +64,7 @@ using GLMakie
 using BioStructures
 struc = retrievepdb("2vb1") |> Observable
 ## or
-struc = read("2vb1.pdb", BioStructures.PDB) |> Observable
+struc = read("2vb1.pdb", BioStructures.PDBFormat) |> Observable
 
 fig = Figure()
 plotstruc!(fig, struc; plottype = :ballandstick, gridposition = (1,1), atomcolors = aquacolors)

diff --git a/src/bonds.jl b/src/bonds.jl
@@ -489,7 +489,7 @@ end
 """
 	getbonds( chn::BioStructures.Chain, selectors... ) -> BitMatrix
 	getbonds( modl::BioStructures.Model, selectors... ) -> BitMatrix
-	getbonds( struc::BioStructures.ProteinStructure, selectors... ) -> BitMatrix
+	getbonds( struc::BioStructures.MolecularStructure, selectors... ) -> BitMatrix
 
 Returns a matrix of all bonds in `chn`, where Mat[i,j] = 1 if atoms i and j are bonded. 
 
@@ -678,7 +678,7 @@ function getbonds(modl::BioStructures.Model, selectors...;
 
 	return nothing
 end
-function getbonds(struc::BioStructures.ProteinStructure, selectors...;
+function getbonds(struc::BioStructures.MolecularStructure, selectors...;
 				algo = :knowledgebased, 
 				H = true,
 				cutoff = 1.9,
@@ -1179,7 +1179,7 @@ function bondshapes(chn::BioStructures.Chain; algo = :knowledgebased, distance =
 
     return bshapes
 end
-function bondshapes(struc::BioStructures.ProteinStructure; algo = :knowledgebased, distance = 1.9, bondwidth = 0.2)
+function bondshapes(struc::BioStructures.MolecularStructure; algo = :knowledgebased, distance = 1.9, bondwidth = 0.2)
 	bshapes = Cylinder3{Float32}[]
 	bnds = getbonds(struc; algo = algo, cutoff = distance)
 	atms = BioStructures.collectatoms(struc)
@@ -1274,7 +1274,7 @@ function bondshapes(chn::BioStructures.Chain, bnds::AbstractMatrix; algo = nothi
 
     return bshapes
 end
-function bondshapes(struc::BioStructures.ProteinStructure, bnds::AbstractMatrix; algo = nothing, cutoff = nothing, bondwidth = 0.2)
+function bondshapes(struc::BioStructures.MolecularStructure, bnds::AbstractMatrix; algo = nothing, cutoff = nothing, bondwidth = 0.2)
 	bshapes = Cylinder3{Float32}[]
 	atms = BioStructures.collectatoms(struc)
 

diff --git a/src/structure.jl b/src/structure.jl
@@ -521,7 +521,7 @@ using BioStructures
 struc = retrievepdb("2vb1", dir = "data/") |> Observable
 strucplot = plotstruc!(fig, struc)
 
-struc = read("data/2vb1_mutant1.pdb", BioStructures.PDB) |> Observable
+struc = read("data/2vb1_mutant1.pdb", BioStructures.PDBFormat) |> Observable
 strucplot = plotstruc!(fig, struc)
 
 chain_A = retrievepdb("2vb1", dir = "data/")["A"] |> Observable
@@ -1150,7 +1150,7 @@ using BioStructures
 struc = retrievepdb("2vb1", dir = "data/") |> Observable
 strucplot = plotstruc(struc)
 
-struc = read("data/2vb1_mutant1.pdb", BioStructures.PDB) |> Observable
+struc = read("data/2vb1_mutant1.pdb", BioStructures.PDBFormat) |> Observable
 strucplot = plotstruc(struc)
 
 chain_A = retrievepdb("2hhb", dir = "data/")["A"] |> Observable